We developed a new Monte Carlo simulator that can incorporate anomalous diffusion and chemical kinetics of intracellular signaling molecules in the dendritic spine. The simulator is based on two well-established Monte Carlo approaches, namely the Kopelman algorithm and the Kinetic Monte Carlo algorithm. This paper describes the basic features of the simulator and compares its performance for th...

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau...

We consider homoepitaxy (or low-misfit heteroepitaxy) via vapor deposition or MBE under UHV conditions. Thin film growth is initiated by nucleation and growth of 2D islands in the submonolayer regime. For atoms subsequently deposited on top of islands, a step edge barrier often inhibits downward transport and produces kinetic roughening during multilayer growth. Such unstable growth is characte...

A fast Monte Carlo simulator with a graphical user interface is an ideal education tool for students learning about molecular beam epitaxy (MBE). This paper discusses the implementation of such a simulator, as well as simulation techniques that may be used to tailor surfaces. Simulations carried out on the learning tool show how MBE can recover step-flow growth, in addition to the temperature d...

Molecular spiders are nanoscale walkers made with catalytic DNA legs attached to a rigid body. They move over a surface of DNA substrates, cleaving them and leaving behind product DNA strands, which they are able to revisit. The legs cleave and detach from substrates more slowly than they detach from products. This difference in residence time and the presence of multiple legs make a spider mov...

We employ an efficient list-based kinetic Monte Carlo (KMC) method to study traffic flow models on one-dimensional (1D) and two-dimensional (2D) lattices based on the exclusion principle and Arrhenius microscopic dynamics. This model implements stochastic rules for cars’ movement based on the configuration of the traffic ahead of each car. In particular, we compare two different lookahead rules...

This article reviews the basic computational techniques for carrying out multiscale simulations using statistical methods, with the focus on simulations of epitaxial growth. First, the statistical-physics background behind Monte Carlo simulations is briefly described. The kinetic Monte Carlo (kMC) method is introduced as an extension of the more wide-spread thermodynamic Monte Carlo methods, an...

We present an efficient Monte Carlo method to simulate reaction–diffusion processes with spatially varying particle annihilation or transformation rates as it occurs for instance in the context of motor-driven intracellular transport. Like Green’s function reaction dynamics and first-passage time methods, our algorithm avoids small diffusive hops by propagating sufficiently distant particles in...

Alexander, Garcia and Alder [1] introduced the Consistent Boltzmann Algorithm (CBA) as a simple variant of Direct Simulation Monte Carlo (DSMC) for dense gases. In CBA, collisions alter both the positions and velocities of the particles. In the present work the limiting kinetic equation for CBA is derived; the formulation is similar to the proof that the Boltzmann equation is the limiting kinet...

– Two mechanisms for the breakdown of step flow growth, in the sense of the appearance of steps of opposite sign to the original vicinality, are studied by kinetic Monte Carlo simulations and scaling arguments. The first mechanism is the nucleation of islands on the terraces, which leads to mound formation if interlayer transport is sufficiently inhibited. The second mechanism is the formation ...